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  • Title: DNAMAT: an efficient graphic matrix sequence homology algorithm and its application to structural analysis.
    Author: Unger R, Harel D, Sussman JL.
    Journal: Comput Appl Biosci; 1986 Dec; 2(4):283-9. PubMed ID: 3450373.
    Abstract:
    We present a fast algorithm to produce a graphic matrix representation of sequence homology. The algorithm is based on lexicographical ordering of fragments. It preserves most of the options of a simple naive algorithm with a significant increase in speed. This algorithm was the bais for a program, called DNAMAT, that has been extensively tested during the last three years at the Weizmann Institute of Science and has proven to be very useful. In addition we suggest a way to extend our approach to analyse a series of related DNA or RNA sequences, in order to determine certain common structural features. The analysis is done by 'summing' a set of dot-matrices to produce an overall matrix that displays structural elements common to most of the sequences. We give an example of this procedure by analysing tRNA sequences.
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